ABSTRACT: In this study, the abundance of major bacterial taxa (based on fluorescent in situ hybridization, FISH) and the structure of the bacterial community (based on denaturing gradient gel electrophoresis, DGGE) were determined in the benthos of 9 streams in the southeastern and midwestern United States and related to differences in environmental conditions. Taxa examined via FISH were Domain Bacteria, Domain Archaea, α-, β-, and γ-Proteobacteria, a portion of the Bacteroidetes (formerly Cytophaga-Flavobacterium-Bacteroides), and Gram-positive bacteria with high (actinobacteria) and low percent guanine+cytosine (GC) content. Of these taxa, generally the most abundant were the β- and α-Proteobacteria, which constituted on average 19.5 and 17.0% of the Domain Bacteria, respectively. Abundance of most taxa was significantly different among streams and sites within a stream. Based on canonical correspondence and correlation analyses, β- and γ-Proteobacteria tended to be most abundant at sites with high dissolved organic carbon (DOC) and nitrate/nitrite concentrations and high benthic organic matter content. In contrast, α-Proteobacteria were more abundant in environments with low DOC and nitrate/nitrite concentrations and low sediment organic carbon content. The other taxa did not exhibit clear correlations with the environmental variables measured. DGGE results revealed that the structure of the bacterial community differed among the streams examined, with limited differences in a given stream and much larger differences among streams. Overall, there were clear differences in community composition that in some cases correlated with differences in environmental conditions.